Variant report

Variant	rs17013734
Chromosome Location	chr4:129746735-129746736
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:129731358..129733912-chr4:129746090..129749523,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000077684	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10518538	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs10857133	1.00[CHB][hapmap]
rs11098988	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098989	0.94[ASN][1000 genomes]
rs11098991	0.83[ASN][1000 genomes]
rs11722253	1.00[CHB][hapmap];0.90[GIH][hapmap]
rs11722830	1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.98[ASN][1000 genomes]
rs11730068	0.85[ASN][1000 genomes]
rs11734137	0.86[ASN][1000 genomes]
rs11735343	1.00[CHB][hapmap]
rs11736731	1.00[CHB][hapmap]
rs11933240	1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.94[ASN][1000 genomes]
rs11940298	0.94[ASN][1000 genomes]
rs11945441	0.88[ASN][1000 genomes]
rs12505447	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13110855	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs13110952	0.85[ASN][1000 genomes]
rs13110956	0.81[ASN][1000 genomes]
rs13111413	1.00[CHB][hapmap]
rs13114904	0.94[ASN][1000 genomes]
rs13125643	0.94[ASN][1000 genomes]
rs13135764	0.83[ASN][1000 genomes]
rs13136807	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13139971	0.94[ASN][1000 genomes]
rs13143989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13146706	0.83[ASN][1000 genomes]
rs13149221	1.00[CHB][hapmap];0.90[GIH][hapmap]
rs13150960	0.82[EUR][1000 genomes]
rs13151322	0.81[CHB][hapmap]
rs34843640	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1020801	chr4:129658178-129778086	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv537248	chr4:129658178-129778086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv517249	chr4:129738328-129927804	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17013734	C4orf33	cis	cerebellum	SCAN
rs17013734	C4orf29	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129734200-129746800	Weak transcription	Fetal Stomach	stomach
2	chr4:129734200-129747000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:129734400-129751600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr4:129734400-129756400	Weak transcription	Aorta	Aorta
5	chr4:129735000-129747000	Weak transcription	Primary B cells from cord blood	blood
6	chr4:129735400-129748200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr4:129735400-129752200	Weak transcription	Fetal Brain Female	brain
8	chr4:129738600-129749200	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr4:129740400-129749200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:129740600-129747000	Weak transcription	Thymus	Thymus
11	chr4:129740800-129748000	Weak transcription	Liver	Liver
12	chr4:129741000-129748600	Weak transcription	Fetal Thymus	thymus
13	chr4:129741200-129746800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:129741200-129748000	Weak transcription	HepG2	liver
15	chr4:129741200-129748200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr4:129741200-129748400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:129741200-129749400	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr4:129741200-129749600	Enhancers	NHDF-Ad	bronchial
19	chr4:129741800-129750000	Weak transcription	Psoas Muscle	Psoas
20	chr4:129741800-129752000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr4:129742000-129746800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr4:129742200-129746800	Weak transcription	Fetal Lung	lung
23	chr4:129743200-129749800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:129743400-129749600	Enhancers	Osteobl	bone
25	chr4:129744000-129747000	Enhancers	Hela-S3	cervix
26	chr4:129744000-129748600	Enhancers	HSMM	muscle
27	chr4:129744200-129747400	Enhancers	Muscle Satellite Cultured Cells	--
28	chr4:129744400-129746800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr4:129744600-129747600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:129744800-129751600	Weak transcription	HUVEC	blood vessel
31	chr4:129745000-129746800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr4:129745000-129749200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:129745000-129751200	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr4:129745200-129749800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:129745400-129747400	Enhancers	Placenta	Placenta
36	chr4:129745600-129746800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:129745600-129747400	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr4:129745600-129747400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:129745600-129747400	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr4:129745600-129748800	Enhancers	Fetal Intestine Large	intestine
41	chr4:129745600-129749000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr4:129745600-129749000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr4:129745800-129747000	Enhancers	NHEK	skin
44	chr4:129745800-129747600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr4:129745800-129749600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr4:129745800-129749800	Enhancers	Fetal Heart	heart
47	chr4:129745800-129749800	Enhancers	NHLF	lung
48	chr4:129746000-129747000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr4:129746000-129747200	Enhancers	Primary T cells from cord blood	blood
50	chr4:129746000-129747200	Enhancers	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links